4DGL | pdb_00004dgl

Crystal Structure of the CK2 Tetrameric Holoenzyme

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4dgld_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Protein kinase CK2, alpha subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4dglc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Protein kinase CK2, alpha subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4dglb_	Small proteins	Rubredoxin-like	Casein kinase II beta subunit	Casein kinase II beta subunit	Casein kinase II beta subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4dgla_	Small proteins	Rubredoxin-like	Casein kinase II beta subunit	Casein kinase II beta subunit	Casein kinase II beta subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039449	3000066	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039449	3000066	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Casein kinase II beta subunit	8039162	3001271	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Casein kinase II beta subunit	8039162	3001271	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e4dglD2	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Pkinase, Kdo	F:	ECOD (20:10:01)
C		e4dglC1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: ADH_zinc_N	F:	ECOD (20:10:01)
B		e4dglB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: FtsJ	F:	ECOD (20:10:01)
A		e4dglA1	A: Rubredoxin-like	X: Rubredoxin-related	H: Casein kinase II beta subunit	T: CK_II_beta	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.1820.10	Mainly Alpha	Orthogonal Bundle	protein kinase ck2 holoenzyme, chain C, domain 1	protein kinase ck2 holoenzyme, chain C, domain 1	CATH (4.3.0)
B	2.20.25.20	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
A	1.10.1820.10	Mainly Alpha	Orthogonal Bundle	protein kinase ck2 holoenzyme, chain C, domain 1	protein kinase ck2 holoenzyme, chain C, domain 1	CATH (4.3.0)
A	2.20.25.20	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
A, B	PF01214	Casein kinase II regulatory subunit (CK_II_beta)	Casein kinase II regulatory subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Casein kinase II subunit alpha	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cellular process regulation of DNA recombination regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair negative regulation of response to stimulus negative regulation of metabolic process DNA recombination primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination regulation of response to stimulus metabolic process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process protein biosynthetic process post-transcriptional regulation of gene expression negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of biosynthetic process regulation of protein metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of protein stability regulation of biological quality protein stabilization protein folding protein maturation apoptotic process cell death programmed cell death catabolic process positive regulation of protein metabolic process macromolecule catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process signaling signal transduction cell communication proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process proteasomal protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of signaling regulation of signal transduction regulation of programmed cell death negative regulation of cell communication negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of programmed cell death regulation of apoptotic process negative regulation of signal transduction apoptotic signaling pathway negative regulation of apoptotic process regulation of cell communication regulation of apoptotic signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway positive regulation of signaling positive regulation of autophagy macroautophagy autophagy regulation of aggrephagy regulation of autophagy positive regulation of aggrephagy regulation of macroautophagy aggrephagy positive regulation of macroautophagy process utilizing autophagic mechanism symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cell PML body disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure rhythmic process negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator signal transduction by p53 class mediator regulation of chromosome segregation regulation of cell cycle process chromosome separation regulation of chromosome separation cell cycle regulation of cell cycle chromosome segregation cell cycle process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex Sin3-type complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular membrane-bounded organelle intracellular organelle lumen histone deacetylase complex intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol cell periphery plasma membrane membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein kinase CK2 complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex nuclear body PML body
A, B	Casein kinase II subunit beta	protein binding binding protein domain specific binding signaling receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding protein-macromolecule adaptor activity molecular adaptor activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity protein binding binding protein domain specific binding signaling receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding protein-macromolecule adaptor activity molecular adaptor activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity cation binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis developmental process multicellular organismal process epithelium development endothelium development tube development morphogenesis of an endothelium endothelial tube morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure development epithelial tube morphogenesis catabolic process negative regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process response to endogenous stimulus adiponectin-activated signaling pathway response to cytokine hormone-mediated signaling pathway cytokine-mediated signaling pathway response to peptide cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular response to cytokine stimulus cellular response to hormone stimulus negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration negative regulation of cell motility blood vessel endothelial cell migration cell migration cell motility locomotion negative regulation of cell migration negative regulation of viral process regulation of viral process regulation of viral life cycle negative regulation of viral life cycle viral process viral life cycle symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cell PML body disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation Wnt signaling pathway positive regulation of activin receptor signaling pathway activin receptor signaling pathway transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle perinuclear theca cytoskeleton perinuclear region of cytoplasm membraneless organelle intracellular membraneless organelle cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen chromatin chromosome cell periphery external encapsulating structure glycocalyx sperm glycocalyx vesicle lumen cytoplasmic vesicle lumen secretory granule lumen protein kinase complex transferase complex, transferring phosphorus-containing groups protein kinase CK2 complex protein-containing complex catalytic complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex nucleolus fibrillar center nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR045216	Casein Kinase 2, subunit alpha	Family
C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
C, D	IPR000719	Protein kinase domain	Domain
C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A, B	IPR000704	Casein kinase II, regulatory subunit	Family
A, B	IPR016149	Casein kinase II, regulatory subunit, N-terminal	Homologous Superfamily
A, B	IPR035991	Casein kinase II subunit beta-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P68400	squamous cell carcinoma adult T-cell leukemia/lymphoma Okur-Chung neurodevelopmental syndrome skin cancer intellectual disability skin neoplasm acute T cell leukemia large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer non-small cell lung carcinoma ovarian cancer Malformations of Cortical Development squamous cell carcinoma adult T-cell leukemia/lymphoma Okur-Chung neurodevelopmental syndrome skin cancer intellectual disability skin neoplasm acute T cell leukemia large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer non-small cell lung carcinoma ovarian cancer Malformations of Cortical Development pancreatic intraductal papillary-mucinous neoplasm
A, B	Pharos: P67870	squamous cell carcinoma adult T-cell leukemia/lymphoma skin neoplasm skin cancer systemic lupus erythematosus acute T cell leukemia cancer Crohn disease Epileptic encephalopathy intellectual disability lung carcinoma rheumatoid arthritis cervical cancer cutaneous lupus erythematosus Hashimoto thyroiditis squamous cell carcinoma adult T-cell leukemia/lymphoma skin neoplasm skin cancer systemic lupus erythematosus acute T cell leukemia cancer Crohn disease Epileptic encephalopathy intellectual disability lung carcinoma rheumatoid arthritis cervical cancer cutaneous lupus erythematosus Hashimoto thyroiditis laryngeal squamous cell carcinoma membranous glomerulonephritis squamous cell lung carcinoma autism spectrum disorder chronic obstructive pulmonary disease epilepsy hypertensive disorder lung adenocarcinoma psoriatic arthritis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.